A modified onboard neuro-fuzzy adaptive (NFA) helicopter turboshaft engine (HTE) automatic control system (ACS) is proposed, which is based on a circuit consisting of a research object, a regulator, an emulator, a compensator, and an observer unit. In this scheme, it is proposed to use the proposed AFNN six-layer hybrid neuro-fuzzy network (NFN) with Sugeno fuzzy inference and a Gaussian membership function for fuzzy variables, which makes it possible to reduce the HTE fuel consumption parameter transient process regulation time by 15.0 times compared with the use of a traditional system automatic control (clear control), 17.5 times compared with the use of a fuzzy ACS (fuzzy control), and 11.25 times compared with the use of a neuro-fuzzy reconfigured ACS based on an ANFIS five-layer hybrid NFN. By applying the Lyapunov method as a criterion, its system stability is proven at any time, with the exception of the initial time, since at the initial time the system is in an equilibrium state. The use of the six-layer ANFF NFN made it possible to reduce the I and II types of error in the HTE fuel consumption controlling task by 1.36…2.06 times compared with the five-layer ANFIS NFN. This work also proposes an AFNN six-layer hybrid NFN training algorithm, which, due to adaptive elements, allows one to change its parameters and settings in real time based on changing conditions or external influences and, as a result, achieve an accuracy of up to 99.98% in the HTE fuel consumption controlling task and reduce losses to 0.2%.